There's definitely issues with AppTrap on Mountain Lion. I've been running into the exact same issues. I've been looking into fixing them, but I've had little time now that I'm finishing up my degree.
I've got a bunch of ideas that I want to implement, but I've had a frustratingly small amount of time to work on my own projects. I know I can't ask for anything from all of you, given that you've all been very patient with me in the past. I can assure you that a new and better version of AppTrap will come.